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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 46 | Line 46
46   * @time 13:51am
47   * @version 1.0
48   */
49 + #include <exception>
50 + #include <iostream>
51 + #include <sstream>
52 + #include <string>
53  
50 – #include <sprng.h>
51 –
54   #include "brains/MoleculeCreator.hpp"
55   #include "brains/SimCreator.hpp"
56   #include "brains/SimSnapshotManager.hpp"
57   #include "io/DumpReader.hpp"
56 – #include "io/parse_me.h"
58   #include "UseTheForce/ForceFieldFactory.hpp"
59   #include "utils/simError.h"
60   #include "utils/StringUtils.hpp"
61 + #include "math/SeqRandNumGen.hpp"
62 + #include "mdParser/MDLexer.hpp"
63 + #include "mdParser/MDParser.hpp"
64 + #include "mdParser/MDTreeParser.hpp"
65 + #include "mdParser/SimplePreprocessor.hpp"
66 + #include "antlr/ANTLRException.hpp"
67 + #include "antlr/TokenStreamRecognitionException.hpp"
68 + #include "antlr/TokenStreamIOException.hpp"
69 + #include "antlr/TokenStreamException.hpp"
70 + #include "antlr/RecognitionException.hpp"
71 + #include "antlr/CharStreamException.hpp"
72 +
73 + #include "antlr/MismatchedCharException.hpp"
74 + #include "antlr/MismatchedTokenException.hpp"
75 + #include "antlr/NoViableAltForCharException.hpp"
76 + #include "antlr/NoViableAltException.hpp"
77 +
78   #ifdef IS_MPI
79 < #include "io/mpiBASS.h"
62 < #include "math/randomSPRNG.hpp"
79 > #include "math/ParallelRandNumGen.hpp"
80   #endif
81  
82   namespace oopse {
83 +  
84 +  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85 +    Globals* simParams = NULL;
86 +    try {
87  
88 < void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
88 >      // Create a preprocessor that preprocesses md file into an ostringstream
89 >      std::stringstream ppStream;
90 > #ifdef IS_MPI            
91 >      int streamSize;
92 >      const int masterNode = 0;
93 >      int commStatus;
94 >      if (worldRank == masterNode) {
95 > #endif
96 >                
97 >        SimplePreprocessor preprocessor;
98 >        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
99 >                
100 > #ifdef IS_MPI            
101 >        //brocasting the stream size
102 >        streamSize = ppStream.str().size() +1;
103 >        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
104  
105 < #ifdef IS_MPI
105 >        commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106 >            
107 >                
108 >      } else {
109 >        //get stream size
110 >        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
111 >                
112 >        char* buf = new char[streamSize];
113 >        assert(buf);
114 >                
115 >        //receive file content
116 >        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117 >                
118 >        ppStream.str(buf);
119 >        delete buf;
120  
121 <    if (worldRank == 0) {
122 < #endif // is_mpi
121 >      }
122 > #endif            
123 >      // Create a scanner that reads from the input stream
124 >      MDLexer lexer(ppStream);
125 >      lexer.setFilename(filename);
126 >      lexer.initDeferredLineCount();
127 >    
128 >      // Create a parser that reads from the scanner
129 >      MDParser parser(lexer);
130 >      parser.setFilename(filename);
131  
132 <        simParams->initalize();
133 <        set_interface_stamps(stamps, simParams);
132 >      // Create an observer that synchorizes file name change
133 >      FilenameObserver observer;
134 >      observer.setLexer(&lexer);
135 >      observer.setParser(&parser);
136 >      lexer.setObserver(&observer);
137 >    
138 >      antlr::ASTFactory factory;
139 >      parser.initializeASTFactory(factory);
140 >      parser.setASTFactory(&factory);
141 >      parser.mdfile();
142  
143 < #ifdef IS_MPI
143 >      // Create a tree parser that reads information into Globals
144 >      MDTreeParser treeParser;
145 >      treeParser.initializeASTFactory(factory);
146 >      treeParser.setASTFactory(&factory);
147 >      simParams = treeParser.walkTree(parser.getAST());
148 >    }
149  
150 <        mpiEventInit();
150 >      
151 >    catch(antlr::MismatchedCharException& e) {
152 >      sprintf(painCave.errMsg,
153 >              "parser exception: %s %s:%d:%d\n",
154 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
155 >      painCave.isFatal = 1;
156 >      simError();          
157 >    }
158 >    catch(antlr::MismatchedTokenException &e) {
159 >      sprintf(painCave.errMsg,
160 >              "parser exception: %s %s:%d:%d\n",
161 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
162 >      painCave.isFatal = 1;
163 >      simError();  
164 >    }
165 >    catch(antlr::NoViableAltForCharException &e) {
166 >      sprintf(painCave.errMsg,
167 >              "parser exception: %s %s:%d:%d\n",
168 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
169 >      painCave.isFatal = 1;
170 >      simError();  
171 >    }
172 >    catch(antlr::NoViableAltException &e) {
173 >      sprintf(painCave.errMsg,
174 >              "parser exception: %s %s:%d:%d\n",
175 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
176 >      painCave.isFatal = 1;
177 >      simError();  
178 >    }
179 >      
180 >    catch(antlr::TokenStreamRecognitionException& e) {
181 >      sprintf(painCave.errMsg,
182 >              "parser exception: %s %s:%d:%d\n",
183 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184 >      painCave.isFatal = 1;
185 >      simError();  
186 >    }
187 >        
188 >    catch(antlr::TokenStreamIOException& e) {
189 >      sprintf(painCave.errMsg,
190 >              "parser exception: %s\n",
191 >              e.getMessage().c_str());
192 >      painCave.isFatal = 1;
193 >      simError();
194 >    }
195 >        
196 >    catch(antlr::TokenStreamException& e) {
197 >      sprintf(painCave.errMsg,
198 >              "parser exception: %s\n",
199 >              e.getMessage().c_str());
200 >      painCave.isFatal = 1;
201 >      simError();
202 >    }        
203 >    catch (antlr::RecognitionException& e) {
204 >      sprintf(painCave.errMsg,
205 >              "parser exception: %s %s:%d:%d\n",
206 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
207 >      painCave.isFatal = 1;
208 >      simError();          
209 >    }
210 >    catch (antlr::CharStreamException& e) {
211 >      sprintf(painCave.errMsg,
212 >              "parser exception: %s\n",
213 >              e.getMessage().c_str());
214 >      painCave.isFatal = 1;
215 >      simError();        
216 >    }
217 >    catch (OOPSEException& e) {
218 >      sprintf(painCave.errMsg,
219 >              "%s\n",
220 >              e.getMessage().c_str());
221 >      painCave.isFatal = 1;
222 >      simError();
223 >    }
224 >    catch (std::exception& e) {
225 >      sprintf(painCave.errMsg,
226 >              "parser exception: %s\n",
227 >              e.what());
228 >      painCave.isFatal = 1;
229 >      simError();
230 >    }
231  
232 < #endif
232 >    return simParams;
233 >  }
234 >  
235 >  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236 >                                  bool loadInitCoords) {
237  
238 <        yacc_BASS(mdFileName.c_str());
238 >    const int bufferSize = 65535;
239 >    char buffer[bufferSize];
240 >    int lineNo = 0;
241 >    std::string mdRawData;
242 >    int metaDataBlockStart = -1;
243 >    int metaDataBlockEnd = -1;
244 >    int i;
245 >    int mdOffset;
246  
247 < #ifdef IS_MPI
247 > #ifdef IS_MPI            
248 >    const int masterNode = 0;
249 >    if (worldRank == masterNode) {
250 > #endif
251  
252 <        throwMPIEvent(NULL);
253 <    } else {
254 <        set_interface_stamps(stamps, simParams);
255 <        mpiEventInit();
256 <        MPIcheckPoint();
257 <        mpiEventLoop();
258 <    }
252 >      std::ifstream mdFile_(mdFileName.c_str());
253 >      
254 >      if (mdFile_.fail()) {
255 >        sprintf(painCave.errMsg,
256 >                "SimCreator: Cannot open file: %s\n",
257 >                mdFileName.c_str());
258 >        painCave.isFatal = 1;
259 >        simError();
260 >      }
261  
262 < #endif
262 >      mdFile_.getline(buffer, bufferSize);
263 >      ++lineNo;
264 >      std::string line = trimLeftCopy(buffer);
265 >      i = CaseInsensitiveFind(line, "<OOPSE");
266 >      if (i == string::npos) {
267 >        sprintf(painCave.errMsg,
268 >                "SimCreator: File: %s is not an OOPSE file!\n",
269 >                mdFileName.c_str());
270 >        painCave.isFatal = 1;
271 >        simError();
272 >      }
273  
274 < }
274 >      //scan through the input stream and find MetaData tag        
275 >      while(mdFile_.getline(buffer, bufferSize)) {
276 >        ++lineNo;
277 >        
278 >        std::string line = trimLeftCopy(buffer);
279 >        if (metaDataBlockStart == -1) {
280 >          i = CaseInsensitiveFind(line, "<MetaData>");
281 >          if (i != string::npos) {
282 >            metaDataBlockStart = lineNo;
283 >            mdOffset = mdFile_.tellg();
284 >          }
285 >        } else {
286 >          i = CaseInsensitiveFind(line, "</MetaData>");
287 >          if (i != string::npos) {
288 >            metaDataBlockEnd = lineNo;
289 >          }
290 >        }
291 >      }
292  
293 < SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
294 <    
295 <    MakeStamps * stamps = new MakeStamps();
293 >      if (metaDataBlockStart == -1) {
294 >        sprintf(painCave.errMsg,
295 >                "SimCreator: File: %s did not contain a <MetaData> tag!\n",
296 >                mdFileName.c_str());
297 >        painCave.isFatal = 1;
298 >        simError();
299 >      }
300 >      if (metaDataBlockEnd == -1) {
301 >        sprintf(painCave.errMsg,
302 >                "SimCreator: File: %s did not contain a closed MetaData block!\n",
303 >                mdFileName.c_str());
304 >        painCave.isFatal = 1;
305 >        simError();
306 >      }
307 >        
308 >      mdFile_.clear();
309 >      mdFile_.seekg(0);
310 >      mdFile_.seekg(mdOffset);
311  
312 <    Globals * simParams = new Globals();
312 >      mdRawData.clear();
313  
314 <    //parse meta-data file
315 <    parseFile(mdFileName, stamps, simParams);
314 >      for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
315 >        mdFile_.getline(buffer, bufferSize);
316 >        mdRawData += buffer;
317 >        mdRawData += "\n";
318 >      }
319  
320 <    //create the force field
321 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
322 <                          simParams->getForceField());
320 >      mdFile_.close();
321 >
322 > #ifdef IS_MPI
323 >    }
324 > #endif
325 >
326 >    std::stringstream rawMetaDataStream(mdRawData);
327 >
328 >    //parse meta-data file
329 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
330      
331 +    //create the force field
332 +    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
333 +
334      if (ff == NULL) {
335 <        sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
336 <                simParams->getForceField());
337 <        painCave.isFatal = 1;
338 <        simError();
335 >      sprintf(painCave.errMsg,
336 >              "ForceField Factory can not create %s force field\n",
337 >              simParams->getForceField().c_str());
338 >      painCave.isFatal = 1;
339 >      simError();
340      }
341 <
341 >    
342      if (simParams->haveForceFieldFileName()) {
343 <        ff->setForceFieldFileName(simParams->getForceFieldFileName());
343 >      ff->setForceFieldFileName(simParams->getForceFieldFileName());
344      }
345      
346      std::string forcefieldFileName;
347      forcefieldFileName = ff->getForceFieldFileName();
348 <
348 >    
349      if (simParams->haveForceFieldVariant()) {
350 <        //If the force field has variant, the variant force field name will be
351 <        //Base.variant.frc. For exampel EAM.u6.frc
352 <        
353 <        std::string variant = simParams->getForceFieldVariant();
354 <
355 <        std::string::size_type pos = forcefieldFileName.rfind(".frc");
356 <        variant = "." + variant;
357 <        if (pos != std::string::npos) {
358 <            forcefieldFileName.insert(pos, variant);
359 <        } else {
360 <            //If the default force field file name does not containt .frc suffix, just append the .variant
361 <            forcefieldFileName.append(variant);
362 <        }
350 >      //If the force field has variant, the variant force field name will be
351 >      //Base.variant.frc. For exampel EAM.u6.frc
352 >      
353 >      std::string variant = simParams->getForceFieldVariant();
354 >      
355 >      std::string::size_type pos = forcefieldFileName.rfind(".frc");
356 >      variant = "." + variant;
357 >      if (pos != std::string::npos) {
358 >        forcefieldFileName.insert(pos, variant);
359 >      } else {
360 >        //If the default force field file name does not containt .frc suffix, just append the .variant
361 >        forcefieldFileName.append(variant);
362 >      }
363      }
364      
365      ff->parse(forcefieldFileName);
366 <    
144 <    //extract the molecule stamps
145 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146 <    compList(stamps, simParams, moleculeStampPairs);
147 <
366 >    ff->setFortranForceOptions();
367      //create SimInfo
368 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
368 >    SimInfo * info = new SimInfo(ff, simParams);
369  
370 <    //gather parameters (SimCreator only retrieves part of the parameters)
370 >    info->setRawMetaData(mdRawData);
371 >    
372 >    //gather parameters (SimCreator only retrieves part of the
373 >    //parameters)
374      gatherParameters(info, mdFileName);
375 <
375 >    
376      //divide the molecules and determine the global index of molecules
377   #ifdef IS_MPI
378      divideMolecules(info);
379   #endif
380 <
380 >    
381      //create the molecules
382      createMolecules(info);
383 <
384 <
385 <    //allocate memory for DataStorage(circular reference, need to break it)
383 >    
384 >    
385 >    //allocate memory for DataStorage(circular reference, need to
386 >    //break it)
387      info->setSnapshotManager(new SimSnapshotManager(info));
388      
389 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
390 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
391 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
389 >    //set the global index of atoms, rigidbodies and cutoffgroups
390 >    //(only need to be set once, the global index will never change
391 >    //again). Local indices of atoms and rigidbodies are already set
392 >    //by MoleculeCreator class which actually delegates the
393 >    //responsibility to LocalIndexManager.
394      setGlobalIndex(info);
395 <
396 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
397 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
398 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
399 <    //we can determine the beginning global indices of atoms before they get created.
395 >    
396 >    //Although addExcludePairs is called inside SimInfo's addMolecule
397 >    //method, at that point atoms don't have the global index yet
398 >    //(their global index are all initialized to -1).  Therefore we
399 >    //have to call addExcludePairs explicitly here. A way to work
400 >    //around is that we can determine the beginning global indices of
401 >    //atoms before they get created.
402      SimInfo::MoleculeIterator mi;
403      Molecule* mol;
404      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
405 <        info->addExcludePairs(mol);
405 >      info->addExcludePairs(mol);
406      }
407      
181 –
182 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183 –    //eta, chi for NPT integrator)
408      if (loadInitCoords)
409 <        loadCoordinates(info);    
409 >      loadCoordinates(info, mdFileName);    
410      
411      return info;
412 < }
413 <
414 < void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
415 <
416 <    //setup seed for random number generator
193 <    int seedValue;
194 <    Globals * simParams = info->getSimParams();
195 <
196 <    if (simParams->haveSeed()) {
197 <        seedValue = simParams->getSeed();
198 <
199 <        if (seedValue < 100000000 ) {
200 <            sprintf(painCave.errMsg,
201 <                    "Seed for sprng library should contain at least 9 digits\n"
202 <                        "OOPSE will generate a seed for user\n");
203 <
204 <            painCave.isFatal = 0;
205 <            simError();
206 <
207 <            //using seed generated by system instead of invalid seed set by user
208 <
209 < #ifndef IS_MPI
210 <
211 <            seedValue = make_sprng_seed();
212 <
213 < #else
214 <
215 <            if (worldRank == 0) {
216 <                seedValue = make_sprng_seed();
217 <            }
218 <
219 <            MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220 <
221 < #endif
222 <
223 <        } //end if (seedValue /1000000000 == 0)
224 <    } else {
225 <
226 < #ifndef IS_MPI
227 <
228 <        seedValue = make_sprng_seed();
229 <
230 < #else
231 <
232 <        if (worldRank == 0) {
233 <            seedValue = make_sprng_seed();
234 <        }
235 <
236 <        MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237 <
238 < #endif
239 <
240 <    } //end of simParams->haveSeed()
241 <
242 <    info->setSeed(seedValue);
243 <
244 <
245 <    //figure out the ouput file names
412 >  }
413 >  
414 >  void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
415 >    
416 >    //figure out the output file names
417      std::string prefix;
418 <
418 >    
419   #ifdef IS_MPI
420 <
420 >    
421      if (worldRank == 0) {
422   #endif // is_mpi
423 <
424 <        if (simParams->haveFinalConfig()) {
425 <            prefix = getPrefix(simParams->getFinalConfig());
426 <        } else {
427 <            prefix = getPrefix(mdfile);
428 <        }
429 <
430 <        info->setFinalConfigFileName(prefix + ".eor");
431 <        info->setDumpFileName(prefix + ".dump");
432 <        info->setStatFileName(prefix + ".stat");
433 <
423 >      Globals * simParams = info->getSimParams();
424 >      if (simParams->haveFinalConfig()) {
425 >        prefix = getPrefix(simParams->getFinalConfig());
426 >      } else {
427 >        prefix = getPrefix(mdfile);
428 >      }
429 >      
430 >      info->setFinalConfigFileName(prefix + ".eor");
431 >      info->setDumpFileName(prefix + ".dump");
432 >      info->setStatFileName(prefix + ".stat");
433 >      info->setRestFileName(prefix + ".zang");
434 >      
435   #ifdef IS_MPI
436 <
436 >      
437      }
438 <
438 >    
439   #endif
440 <
441 < }
442 <
440 >    
441 >  }
442 >  
443   #ifdef IS_MPI
444 < void SimCreator::divideMolecules(SimInfo *info) {
445 <    double numerator;
446 <    double denominator;
447 <    double precast;
448 <    double x;
449 <    double y;
450 <    double a;
444 >  void SimCreator::divideMolecules(SimInfo *info) {
445 >    RealType numerator;
446 >    RealType denominator;
447 >    RealType precast;
448 >    RealType x;
449 >    RealType y;
450 >    RealType a;
451      int old_atoms;
452      int add_atoms;
453      int new_atoms;
# Line 287 | Line 459 | void SimCreator::divideMolecules(SimInfo *info) {
459      int which_proc;
460      int nProcessors;
461      std::vector<int> atomsPerProc;
290 –    randomSPRNG myRandom(info->getSeed());
462      int nGlobalMols = info->getNGlobalMolecules();
463      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
464      
465      MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
466 <
466 >    
467      if (nProcessors > nGlobalMols) {
468 <        sprintf(painCave.errMsg,
469 <                "nProcessors (%d) > nMol (%d)\n"
470 <                    "\tThe number of processors is larger than\n"
471 <                    "\tthe number of molecules.  This will not result in a \n"
472 <                    "\tusable division of atoms for force decomposition.\n"
473 <                    "\tEither try a smaller number of processors, or run the\n"
474 <                    "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
475 <
476 <        painCave.isFatal = 1;
477 <        simError();
478 <    }
479 <
468 >      sprintf(painCave.errMsg,
469 >              "nProcessors (%d) > nMol (%d)\n"
470 >              "\tThe number of processors is larger than\n"
471 >              "\tthe number of molecules.  This will not result in a \n"
472 >              "\tusable division of atoms for force decomposition.\n"
473 >              "\tEither try a smaller number of processors, or run the\n"
474 >              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
475 >      
476 >      painCave.isFatal = 1;
477 >      simError();
478 >    }
479 >    
480 >    int seedValue;
481 >    Globals * simParams = info->getSimParams();
482 >    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
483 >    if (simParams->haveSeed()) {
484 >      seedValue = simParams->getSeed();
485 >      myRandom = new SeqRandNumGen(seedValue);
486 >    }else {
487 >      myRandom = new SeqRandNumGen();
488 >    }  
489 >    
490 >    
491      a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
492 <
492 >    
493      //initialize atomsPerProc
494      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
495 <
495 >    
496      if (worldRank == 0) {
497 <        numerator = info->getNGlobalAtoms();
498 <        denominator = nProcessors;
499 <        precast = numerator / denominator;
500 <        nTarget = (int)(precast + 0.5);
501 <
502 <        for(i = 0; i < nGlobalMols; i++) {
503 <            done = 0;
504 <            loops = 0;
505 <
506 <            while (!done) {
507 <                loops++;
508 <
509 <                // Pick a processor at random
510 <
511 <                which_proc = (int) (myRandom.getRandom() * nProcessors);
512 <
513 <                //get the molecule stamp first
514 <                int stampId = info->getMoleculeStampId(i);
515 <                MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
516 <
517 <                // How many atoms does this processor have so far?
518 <                old_atoms = atomsPerProc[which_proc];
519 <                add_atoms = moleculeStamp->getNAtoms();
520 <                new_atoms = old_atoms + add_atoms;
521 <
522 <                // If we've been through this loop too many times, we need
523 <                // to just give up and assign the molecule to this processor
524 <                // and be done with it.
525 <
526 <                if (loops > 100) {
527 <                    sprintf(painCave.errMsg,
528 <                            "I've tried 100 times to assign molecule %d to a "
529 <                                " processor, but can't find a good spot.\n"
530 <                                "I'm assigning it at random to processor %d.\n",
531 <                            i, which_proc);
532 <
533 <                    painCave.isFatal = 0;
534 <                    simError();
535 <
536 <                    molToProcMap[i] = which_proc;
537 <                    atomsPerProc[which_proc] += add_atoms;
538 <
539 <                    done = 1;
540 <                    continue;
541 <                }
542 <
543 <                // If we can add this molecule to this processor without sending
544 <                // it above nTarget, then go ahead and do it:
545 <
546 <                if (new_atoms <= nTarget) {
547 <                    molToProcMap[i] = which_proc;
548 <                    atomsPerProc[which_proc] += add_atoms;
549 <
550 <                    done = 1;
551 <                    continue;
552 <                }
553 <
554 <                // The only situation left is when new_atoms > nTarget.  We
555 <                // want to accept this with some probability that dies off the
556 <                // farther we are from nTarget
557 <
558 <                // roughly:  x = new_atoms - nTarget
559 <                //           Pacc(x) = exp(- a * x)
560 <                // where a = penalty / (average atoms per molecule)
561 <
562 <                x = (double)(new_atoms - nTarget);
563 <                y = myRandom.getRandom();
564 <
565 <                if (y < exp(- a * x)) {
566 <                    molToProcMap[i] = which_proc;
567 <                    atomsPerProc[which_proc] += add_atoms;
568 <
569 <                    done = 1;
570 <                    continue;
571 <                } else {
572 <                    continue;
573 <                }
392 <            }
497 >      numerator = info->getNGlobalAtoms();
498 >      denominator = nProcessors;
499 >      precast = numerator / denominator;
500 >      nTarget = (int)(precast + 0.5);
501 >      
502 >      for(i = 0; i < nGlobalMols; i++) {
503 >        done = 0;
504 >        loops = 0;
505 >        
506 >        while (!done) {
507 >          loops++;
508 >          
509 >          // Pick a processor at random
510 >          
511 >          which_proc = (int) (myRandom->rand() * nProcessors);
512 >          
513 >          //get the molecule stamp first
514 >          int stampId = info->getMoleculeStampId(i);
515 >          MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
516 >          
517 >          // How many atoms does this processor have so far?
518 >          old_atoms = atomsPerProc[which_proc];
519 >          add_atoms = moleculeStamp->getNAtoms();
520 >          new_atoms = old_atoms + add_atoms;
521 >          
522 >          // If we've been through this loop too many times, we need
523 >          // to just give up and assign the molecule to this processor
524 >          // and be done with it.
525 >          
526 >          if (loops > 100) {
527 >            sprintf(painCave.errMsg,
528 >                    "I've tried 100 times to assign molecule %d to a "
529 >                    " processor, but can't find a good spot.\n"
530 >                    "I'm assigning it at random to processor %d.\n",
531 >                    i, which_proc);
532 >            
533 >            painCave.isFatal = 0;
534 >            simError();
535 >            
536 >            molToProcMap[i] = which_proc;
537 >            atomsPerProc[which_proc] += add_atoms;
538 >            
539 >            done = 1;
540 >            continue;
541 >          }
542 >          
543 >          // If we can add this molecule to this processor without sending
544 >          // it above nTarget, then go ahead and do it:
545 >          
546 >          if (new_atoms <= nTarget) {
547 >            molToProcMap[i] = which_proc;
548 >            atomsPerProc[which_proc] += add_atoms;
549 >            
550 >            done = 1;
551 >            continue;
552 >          }
553 >          
554 >          // The only situation left is when new_atoms > nTarget.  We
555 >          // want to accept this with some probability that dies off the
556 >          // farther we are from nTarget
557 >          
558 >          // roughly:  x = new_atoms - nTarget
559 >          //           Pacc(x) = exp(- a * x)
560 >          // where a = penalty / (average atoms per molecule)
561 >          
562 >          x = (RealType)(new_atoms - nTarget);
563 >          y = myRandom->rand();
564 >          
565 >          if (y < exp(- a * x)) {
566 >            molToProcMap[i] = which_proc;
567 >            atomsPerProc[which_proc] += add_atoms;
568 >            
569 >            done = 1;
570 >            continue;
571 >          } else {
572 >            continue;
573 >          }
574          }
575 <
576 <        // Spray out this nonsense to all other processors:
577 <
578 <        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
575 >      }
576 >      
577 >      delete myRandom;
578 >      
579 >      // Spray out this nonsense to all other processors:
580 >      
581 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
582      } else {
583 <
584 <        // Listen to your marching orders from processor 0:
585 <
586 <        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
583 >      
584 >      // Listen to your marching orders from processor 0:
585 >      
586 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
587      }
588 <
588 >    
589      info->setMolToProcMap(molToProcMap);
590      sprintf(checkPointMsg,
591              "Successfully divided the molecules among the processors.\n");
592 <    MPIcheckPoint();
593 < }
594 <
592 >    errorCheckPoint();
593 >  }
594 >  
595   #endif
596 <
597 < void SimCreator::createMolecules(SimInfo *info) {
596 >  
597 >  void SimCreator::createMolecules(SimInfo *info) {
598      MoleculeCreator molCreator;
599      int stampId;
600 <
600 >    
601      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
602 <
602 >      
603   #ifdef IS_MPI
604 <
605 <        if (info->getMolToProc(i) == worldRank) {
604 >      
605 >      if (info->getMolToProc(i) == worldRank) {
606   #endif
607 <
608 <            stampId = info->getMoleculeStampId(i);
609 <            Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
610 <                                                                                    stampId, i, info->getLocalIndexManager());
611 <
612 <            info->addMolecule(mol);
613 <
607 >        
608 >        stampId = info->getMoleculeStampId(i);
609 >        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
610 >                                                   stampId, i, info->getLocalIndexManager());
611 >        
612 >        info->addMolecule(mol);
613 >        
614   #ifdef IS_MPI
615 <
616 <        }
617 <
615 >        
616 >      }
617 >      
618   #endif
619 <
619 >      
620      } //end for(int i=0)  
621 < }
622 <
623 < void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
440 <                        std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
441 <    int i;
442 <    char * id;
443 <    MoleculeStamp * currentStamp;
444 <    Component** the_components = simParams->getComponents();
445 <    int n_components = simParams->getNComponents();
446 <
447 <    if (!simParams->haveNMol()) {
448 <        // we don't have the total number of molecules, so we assume it is
449 <        // given in each component
450 <
451 <        for(i = 0; i < n_components; i++) {
452 <            if (!the_components[i]->haveNMol()) {
453 <                // we have a problem
454 <                sprintf(painCave.errMsg,
455 <                        "SimCreator Error. No global NMol or component NMol given.\n"
456 <                            "\tCannot calculate the number of atoms.\n");
457 <
458 <                painCave.isFatal = 1;
459 <                simError();
460 <            }
461 <
462 <            id = the_components[i]->getType();
463 <            currentStamp = (stamps->extractMolStamp(id))->getStamp();
464 <
465 <            if (currentStamp == NULL) {
466 <                sprintf(painCave.errMsg,
467 <                        "SimCreator error: Component \"%s\" was not found in the "
468 <                            "list of declared molecules\n", id);
469 <
470 <                painCave.isFatal = 1;
471 <                simError();
472 <            }
473 <
474 <            moleculeStampPairs.push_back(
475 <                std::make_pair(currentStamp, the_components[i]->getNMol()));
476 <        } //end for (i = 0; i < n_components; i++)
477 <    } else {
478 <        sprintf(painCave.errMsg, "SimSetup error.\n"
479 <                                     "\tSorry, the ability to specify total"
480 <                                     " nMols and then give molfractions in the components\n"
481 <                                     "\tis not currently supported."
482 <                                     " Please give nMol in the components.\n");
483 <
484 <        painCave.isFatal = 1;
485 <        simError();
486 <    }
487 <
488 < #ifdef IS_MPI
489 <
490 <    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
491 <    MPIcheckPoint();
492 <
493 < #endif // is_mpi
494 <
495 < }
496 <
497 < void SimCreator::setGlobalIndex(SimInfo *info) {
621 >  }
622 >    
623 >  void SimCreator::setGlobalIndex(SimInfo *info) {
624      SimInfo::MoleculeIterator mi;
625      Molecule::AtomIterator ai;
626      Molecule::RigidBodyIterator ri;
627      Molecule::CutoffGroupIterator ci;
628 +    Molecule::IntegrableObjectIterator  ioi;
629      Molecule * mol;
630      Atom * atom;
631      RigidBody * rb;
# Line 507 | Line 634 | void SimCreator::setGlobalIndex(SimInfo *info) {
634      int beginRigidBodyIndex;
635      int beginCutoffGroupIndex;
636      int nGlobalAtoms = info->getNGlobalAtoms();
510 –    
511 – #ifndef IS_MPI
637  
638 +    /**@todo fixme */
639 + #ifndef IS_MPI
640 +    
641      beginAtomIndex = 0;
642      beginRigidBodyIndex = 0;
643      beginCutoffGroupIndex = 0;
644 <
644 >    
645   #else
646 <
646 >    
647      int nproc;
648      int myNode;
649 <
649 >    
650      myNode = worldRank;
651      MPI_Comm_size(MPI_COMM_WORLD, &nproc);
652 <
652 >    
653      std::vector < int > tmpAtomsInProc(nproc, 0);
654      std::vector < int > tmpRigidBodiesInProc(nproc, 0);
655      std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
656      std::vector < int > NumAtomsInProc(nproc, 0);
657      std::vector < int > NumRigidBodiesInProc(nproc, 0);
658      std::vector < int > NumCutoffGroupsInProc(nproc, 0);
659 <
659 >    
660      tmpAtomsInProc[myNode] = info->getNAtoms();
661      tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
662      tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
663 <
663 >    
664      //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
665      MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
666                    MPI_SUM, MPI_COMM_WORLD);
# Line 540 | Line 668 | void SimCreator::setGlobalIndex(SimInfo *info) {
668                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
669      MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
670                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671 <
671 >    
672      beginAtomIndex = 0;
673      beginRigidBodyIndex = 0;
674      beginCutoffGroupIndex = 0;
675 <
675 >    
676      for(int i = 0; i < myNode; i++) {
677 <        beginAtomIndex += NumAtomsInProc[i];
678 <        beginRigidBodyIndex += NumRigidBodiesInProc[i];
679 <        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
677 >      beginAtomIndex += NumAtomsInProc[i];
678 >      beginRigidBodyIndex += NumRigidBodiesInProc[i];
679 >      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
680      }
681 <
681 >    
682 > #endif
683 >    
684      //rigidbody's index begins right after atom's
685      beginRigidBodyIndex += info->getNGlobalAtoms();
686 < #endif
557 <
686 >    
687      for(mol = info->beginMolecule(mi); mol != NULL;
688          mol = info->nextMolecule(mi)) {
689 <
690 <        //local index(index in DataStorge) of atom is important
691 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692 <            atom->setGlobalIndex(beginAtomIndex++);
693 <        }
694 <
695 <        for(rb = mol->beginRigidBody(ri); rb != NULL;
696 <            rb = mol->nextRigidBody(ri)) {
697 <            rb->setGlobalIndex(beginRigidBodyIndex++);
698 <        }
699 <
700 <        //local index of cutoff group is trivial, it only depends on the order of travesing
701 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
702 <            cg = mol->nextCutoffGroup(ci)) {
703 <            cg->setGlobalIndex(beginCutoffGroupIndex++);
704 <        }
689 >      
690 >      //local index(index in DataStorge) of atom is important
691 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692 >        atom->setGlobalIndex(beginAtomIndex++);
693 >      }
694 >      
695 >      for(rb = mol->beginRigidBody(ri); rb != NULL;
696 >          rb = mol->nextRigidBody(ri)) {
697 >        rb->setGlobalIndex(beginRigidBodyIndex++);
698 >      }
699 >      
700 >      //local index of cutoff group is trivial, it only depends on the order of travesing
701 >      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
702 >          cg = mol->nextCutoffGroup(ci)) {
703 >        cg->setGlobalIndex(beginCutoffGroupIndex++);
704 >      }
705      }
706 <
706 >    
707      //fill globalGroupMembership
708      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
709      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
710 <        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
711 <
712 <            for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
713 <                globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
714 <            }
715 <
716 <        }      
710 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
711 >        
712 >        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
713 >          globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
714 >        }
715 >        
716 >      }      
717      }
718 <
718 >    
719   #ifdef IS_MPI    
720      // Since the globalGroupMembership has been zero filled and we've only
721      // poked values into the atoms we know, we can do an Allreduce
# Line 596 | Line 725 | void SimCreator::setGlobalIndex(SimInfo *info) {
725      std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
726      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
727                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
728 <     info->setGlobalGroupMembership(tmpGroupMembership);
728 >    info->setGlobalGroupMembership(tmpGroupMembership);
729   #else
730      info->setGlobalGroupMembership(globalGroupMembership);
731   #endif
732 <
732 >    
733      //fill molMembership
734      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
735      
736      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
737 <
738 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
739 <            globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
740 <        }
737 >      
738 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
739 >        globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
740 >      }
741      }
742 <
742 >    
743   #ifdef IS_MPI
744      std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
745 <
745 >    
746      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
747                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
748      
# Line 622 | Line 751 | void SimCreator::setGlobalIndex(SimInfo *info) {
751      info->setGlobalMolMembership(globalMolMembership);
752   #endif
753  
754 < }
754 >    // nIOPerMol holds the number of integrable objects per molecule
755 >    // here the molecules are listed by their global indices.
756  
757 < void SimCreator::loadCoordinates(SimInfo* info) {
757 >    std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
758 >    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
759 >      nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
760 >    }
761 >    
762 > #ifdef IS_MPI
763 >    std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
764 >    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
765 >                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
766 > #else
767 >    std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
768 > #endif    
769 >
770 > std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
771 >
772 > int startingIndex = 0;
773 > for (int i = 0; i < info->getNGlobalMolecules(); i++) {
774 >  startingIOIndexForMol[i] = startingIndex;
775 >  startingIndex += numIntegrableObjectsPerMol[i];
776 > }
777 >
778 > std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
779 > for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
780 >      int myGlobalIndex = mol->getGlobalIndex();
781 >      int globalIO = startingIOIndexForMol[myGlobalIndex];
782 >      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
783 >           integrableObject = mol->nextIntegrableObject(ioi)) {
784 >            integrableObject->setGlobalIntegrableObjectIndex(globalIO);
785 >            IOIndexToIntegrableObject[globalIO] = integrableObject;
786 >            globalIO++;
787 >      }
788 >    }
789 >
790 >  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
791 >  
792 >  }
793 >  
794 >  void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
795      Globals* simParams;
796      simParams = info->getSimParams();
797      
798 <    if (!simParams->haveInitialConfig()) {
799 <        sprintf(painCave.errMsg,
633 <                "Cannot intialize a simulation without an initial configuration file.\n");
634 <        painCave.isFatal = 1;;
635 <        simError();
636 <    }
637 <        
638 <    DumpReader reader(info, simParams->getInitialConfig());
798 >    
799 >    DumpReader reader(info, mdFileName);
800      int nframes = reader.getNFrames();
801 <
801 >    
802      if (nframes > 0) {
803 <        reader.readFrame(nframes - 1);
803 >      reader.readFrame(nframes - 1);
804      } else {
805 <        //invalid initial coordinate file
806 <        sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
807 <                simParams->getInitialConfig());
808 <        painCave.isFatal = 1;
809 <        simError();
805 >      //invalid initial coordinate file
806 >      sprintf(painCave.errMsg,
807 >              "Initial configuration file %s should at least contain one frame\n",
808 >              mdFileName.c_str());
809 >      painCave.isFatal = 1;
810 >      simError();
811      }
812 <
812 >    
813      //copy the current snapshot to previous snapshot
814      info->getSnapshotManager()->advance();
815 < }
816 <
815 >  }
816 >  
817   } //end namespace oopse
818  
819  

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